In the BIOS at boot time, there is an option for disallowing access to
the printer port from the docking station. I set that. (There is an
option to disable the printer port entirely, but I didn’t need to do
that - I just needed to stop the docking station from accessing it.) A
quick save and reboot, and I’m ready to eject from the docking station
at any time - no more error.

Note that I don’t have any printers locally attached to my machine, so
disabling the printer port connection to the docking station didn’t hurt
me. If you have a local printer attached to your docking station, this
may not be the best solution for you.

UPDATE: I am on ThinkPad T60 BIOS version 2.21 and the option is
under Config -> Docking Station. Set the “Legacy Devices on Mini Dock”
setting to “Disabled” to disallow the docking station access to the
parallel port.